October 2009 Volume 16 Number 10, pp 1003 - 1115
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EDITORIAL
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London's hottest new attraction is... scientists at work p1003
doi:10.1038/nsmb1009-1003
Scientists engaging with the public on a more direct level is bound
to benefit both.
http://links.ealert.nature.com/ctt?kn=88&m=34130576&r=MTc2OTcxOTY5MQS2&b=2&j=NTkwMzM4NjAS1&mt=1&rt=0
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NEWS AND VIEWS
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PORE-ing over ERK substrates pp1004 - 1005
Natalie G Ahn
doi:10.1038/nsmb1009-1004
A functional proteomics study reveals that nuclear pore proteins are
direct substrates for mitogen-activated protein (MAP) kinases,
leading to a new mechanism for growth factor control of nuclear
transport.
http://links.ealert.nature.com/ctt?kn=82&m=34130576&r=MTc2OTcxOTY5MQS2&b=2&j=NTkwMzM4NjAS1&mt=1&rt=0
Trigger factor finds new jobs and contacts pp1006 - 1008
Anja Hoffmann and Bernd Bukau
doi:10.1038/nsmb1009-1006
Trigger factor is a ribosome-associated chaperone that assists early
folding steps of nascent proteins in bacteria. A new study presents
the first crystal structure of Trigger factor in complex with a
folded protein bound as substrate, challenges the current model for
how Trigger factor interacts with substrates and suggests an
unexpected role for Trigger factor in protein assembly and ribosome
biogenesis.
http://links.ealert.nature.com/ctt?kn=36&m=34130576&r=MTc2OTcxOTY5MQS2&b=2&j=NTkwMzM4NjAS1&mt=1&rt=0
Silence of the budding yeast p1008
Sabbi Lall
doi:10.1038/nsmb1009-1008
http://links.ealert.nature.com/ctt?kn=38&m=34130576&r=MTc2OTcxOTY5MQS2&b=2&j=NTkwMzM4NjAS1&mt=1&rt=0
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RESEARCH HIGHLIGHTS
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Research highlights p1009
doi:10.1038/nsmb1009-1009
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PERSPECTIVE
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Telomeric circles: universal players in telomere maintenance?
pp1010 - 1015
Lubomir Tomaska, Jozef Nosek, Juraj Kramara and Jack D Griffith
doi:10.1038/nsmb.1660
Abstract: http://links.ealert.nature.com/ctt?kn=43&m=34130576&r=MTc2OTcxOTY5MQS2&b=2&j=NTkwMzM4NjAS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=45&m=34130576&r=MTc2OTcxOTY5MQS2&b=2&j=NTkwMzM4NjAS1&mt=1&rt=0
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ARTICLES
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LIN-28 and the poly(U) polymerase PUP-2 regulate let-7 microRNA
processing in Caenorhabditis elegans pp1016 - 1020
Nicolas J Lehrbach et al.
doi:10.1038/nsmb.1675
Developmental expression of the microRNA let-7 is tightly regulated
in many animals, and turnover has been linked to LIN-28 and
uridylation in mammals. This regulation is now shown to be conserved
in Caenorhabditis elegans, and PUP-2 is shown to be a uridylase that
is specifically recruited to let-7 in a LIN-28-dependent manner.
Abstract: http://links.ealert.nature.com/ctt?kn=47&m=34130576&r=MTc2OTcxOTY5MQS2&b=2&j=NTkwMzM4NjAS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=49&m=34130576&r=MTc2OTcxOTY5MQS2&b=2&j=NTkwMzM4NjAS1&mt=1&rt=0
Lin28 recruits the TUTase Zcchc11 to inhibit let-7 maturation in
mouse embryonic stem cells pp1021 - 1025
John P Hagan, Elena Piskounova and Richard I Gregory
doi:10.1038/nsmb.1676
The let-7 microRNA has been implicated in development and disease.
Its expression must thus be tightly regulated, and previously
uridylation and Lin28 were implicated in let-7 stability. Zcchc11
is now shown to be the uridylase that mediates pre-let-7 modification
and regulates mature let-7 levels and activity in mouse embryonic
stem cells.
Abstract: http://links.ealert.nature.com/ctt?kn=52&m=34130576&r=MTc2OTcxOTY5MQS2&b=2&j=NTkwMzM4NjAS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=54&m=34130576&r=MTc2OTcxOTY5MQS2&b=2&j=NTkwMzM4NjAS1&mt=1&rt=0
Phosphoproteomics reveals new ERK MAP kinase targets and links ERK
to nucleoporin-mediated nuclear transport pp1026 - 1035
Hidetaka Kosako et al.
doi:10.1038/nsmb.1656
An improved method for detecting proteins phosphorylated by the ERK
kinase reveals multiple new in vitro ERK substrates, including three
nucleoporin proteins. Nup50 is phosphorylated in FG repeats by ERK2
in vivo and in vitro, suggesting a new mechanism by which MAP kinase
signaling controls nuclear translocation of proteins.
Abstract: http://links.ealert.nature.com/ctt?kn=56&m=34130576&r=MTc2OTcxOTY5MQS2&b=2&j=NTkwMzM4NjAS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=125&m=34130576&r=MTc2OTcxOTY5MQS2&b=2&j=NTkwMzM4NjAS1&mt=1&rt=0
Active site remodeling switches HIV specificity of antiretroviral
TRIMCyp pp1036 - 1042
Amanda J Price et al.
doi:10.1038/nsmb.1667
Rhesus macaque monkeys can inhibit retroviral replication via
TRIMCyp, a variant of TRIM5a with an insertion of the cyclophilin
A cDNA. Cyclophilin A binds to HIV-1 capsid, whereas TRIMCyp
restricts HIV-2. How the change in specificity of this domain
occurred is now revealed through biophysical and structural
studies.
Abstract: http://links.ealert.nature.com/ctt?kn=122&m=34130576&r=MTc2OTcxOTY5MQS2&b=2&j=NTkwMzM4NjAS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=124&m=34130576&r=MTc2OTcxOTY5MQS2&b=2&j=NTkwMzM4NjAS1&mt=1&rt=0
Distinct promoter dynamics of the basal transcription factor TBP
across the yeast genome pp1043 - 1048
Folkert J van Werven, Hetty A A M van Teeffelen, Frank C P Holstege
and H Th Marc Timmers
doi:10.1038/nsmb.1674
Transcription initiation involves recruitment of key factors to
promoters. Yeast TATA-binding protein (TBP) turnover is now examined
genome-wide and genes transcribed by the three RNA polymerases found
to have distinct signatures. Further analyses suggest that TBP
dynamics, rather than DNA sequence affinity per se, is key to gene
expression.
Abstract: http://links.ealert.nature.com/ctt?kn=120&m=34130576&r=MTc2OTcxOTY5MQS2&b=2&j=NTkwMzM4NjAS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=121&m=34130576&r=MTc2OTcxOTY5MQS2&b=2&j=NTkwMzM4NjAS1&mt=1&rt=0
Following evolutionary paths to protein-protein interactions with
high affinity and selectivity pp1049 - 1055
Kalia Bernath Levin et al.
doi:10.1038/nsmb.1670
Colicins are secreted bacterial toxins. To avoid killing the producer
organism, each colicin is coexpressed with a high-affinity inhibitor,
or immunity protein (Im). The evolution of Im-Colicin interfaces and
the evolvability traits of protein-protein interactions are now
examined using in vitro evolution and structural analyses.
Abstract: http://links.ealert.nature.com/ctt?kn=135&m=34130576&r=MTc2OTcxOTY5MQS2&b=2&j=NTkwMzM4NjAS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=137&m=34130576&r=MTc2OTcxOTY5MQS2&b=2&j=NTkwMzM4NjAS1&mt=1&rt=0
Single-molecule imaging of DNA curtains reveals intrinsic energy
landscapes for nucleosome deposition pp1056 - 1062
Mari-Liis Visnapuu and Eric C Greene
doi:10.1038/nsmb.1655
The positions of nucleosomes can affect processes occurring on DNA.
DNA curtains are now used to study nucleosome positioning in vitro.
This allows assessment of sequence-related effects on positioning
and indicates that the yeast factor Scm3 can overcome the aversion
of nucleosomes to AT-rich sequences.
Abstract: http://links.ealert.nature.com/ctt?kn=131&m=34130576&r=MTc2OTcxOTY5MQS2&b=2&j=NTkwMzM4NjAS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=132&m=34130576&r=MTc2OTcxOTY5MQS2&b=2&j=NTkwMzM4NjAS1&mt=1&rt=0
Structural basis for autoregulation of the zinc transporter YiiP
pp1063 - 1067
Min Lu, Jin Chai and Dax Fu
doi:10.1038/nsmb.1662
Escherichia coli YiiP, a member of the cation diffusion facilitator
family, exports cytoplasmic zinc, maintaining cellular homeostasis.
The high-resolution crystal structure of YiiP, combined with
functional studies focused on its cytoplasmic C-terminal domain,
suggest how it is able to allosterically modulate zinc transport.
Abstract: http://links.ealert.nature.com/ctt?kn=128&m=34130576&r=MTc2OTcxOTY5MQS2&b=2&j=NTkwMzM4NjAS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=99&m=34130576&r=MTc2OTcxOTY5MQS2&b=2&j=NTkwMzM4NjAS1&mt=1&rt=0
High-resolution structure of the rotor ring of a proton-dependent
ATP synthase pp1068 - 1073
Denys Pogoryelov, Ozkan Yildiz, Jose D Faraldo-Gomez and Thomas Meier
doi:10.1038/nsmb.1678
F1Fo ATP synthases produce ATP using proton- or sodium-motive force
to drive ions through the membrane-embedded Fo complex, causing
rotation of its c-ring rotor leading to ATP synthesis. The first
high-resolution crystal structure of the c-ring from a
proton-translocating F1Fo-ATP synthase reveals the architecture of
the proton-binding site and provides insight into the mechanism of
proton transport.
Abstract: http://links.ealert.nature.com/ctt?kn=100&m=34130576&r=MTc2OTcxOTY5MQS2&b=2&j=NTkwMzM4NjAS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=94&m=34130576&r=MTc2OTcxOTY5MQS2&b=2&j=NTkwMzM4NjAS1&mt=1&rt=0
The histone variant macroH2A is an epigenetic regulator of key
developmental genes pp1074 - 1079
Marcus Buschbeck et al.
doi:10.1038/nsmb.1665
Nucleosomes can be modified by replacing the core histones with
variants, the most diverse of which is macroH2A. The localization
of macroH2A variants in human male pluripotent cells indicates that
this variant functions in repression of key developmental genes and
is essential for zebrafish embryogenesis.
Abstract: http://links.ealert.nature.com/ctt?kn=95&m=34130576&r=MTc2OTcxOTY5MQS2&b=2&j=NTkwMzM4NjAS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=96&m=34130576&r=MTc2OTcxOTY5MQS2&b=2&j=NTkwMzM4NjAS1&mt=1&rt=0
Interactions between lipids and voltage sensor paddles detected with
tarantula toxins pp1080 - 1085
Mirela Milescu et al.
doi:10.1038/nsmb.1679
Increasing evidence indicates that membrane protein function can be
affected by the surrounding membrane bilayer. A new study on
voltage-gated potassium channels using tarantula toxins suggests that
lipid interaction with the voltage sensor can influence channel
function.
Abstract: http://links.ealert.nature.com/ctt?kn=97&m=34130576&r=MTc2OTcxOTY5MQS2&b=2&j=NTkwMzM4NjAS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=105&m=34130576&r=MTc2OTcxOTY5MQS2&b=2&j=NTkwMzM4NjAS1&mt=1&rt=0
The execution of the transcriptional axis mutant p53, E2F1 and ID4
promotes tumor neo-angiogenesis pp1086 - 1093
Giulia Fontemaggi et al.
doi:10.1038/nsmb.1669
Some p53 mutations result in gain-of-function variants that can
contribute to tumorigenesis. Three such mutants, R175H, R273H and
R280K p53, are now shown to cooperate with transcription factor E2F1
to upregulate the expression of ID4, which in turn stabilizes the
transcripts from pro-angiogenic factors IL-8 and GRO-alpha.
Abstract: http://links.ealert.nature.com/ctt?kn=107&m=34130576&r=MTc2OTcxOTY5MQS2&b=2&j=NTkwMzM4NjAS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=109&m=34130576&r=MTc2OTcxOTY5MQS2&b=2&j=NTkwMzM4NjAS1&mt=1&rt=0
Splice site strength-dependent activity and genetic buffering by
poly-G runs pp1094 - 1100
Xinshu Xiao et al.
doi:10.1038/nsmb.1661
Alternative splicing increases genome coding potential and is
affected by factors including the hnRNPs. The effect of altering
splice site strength on splicing activity is now found to be
antagonized by nearby hnRNP H binding sites. Other splicing factor
sites may have similar effects and may thus have influenced splice
form evolution.
Abstract: http://links.ealert.nature.com/ctt?kn=111&m=34130576&r=MTc2OTcxOTY5MQS2&b=2&j=NTkwMzM4NjAS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=14&m=34130576&r=MTc2OTcxOTY5MQS2&b=2&j=NTkwMzM4NjAS1&mt=1&rt=0
Structural and kinetic determinants of protease substrates
pp1101 - 1108
John C Timmer et al.
doi:10.1038/nsmb.1668
Identifying physiological substrates of proteases still poses a
challenge. An unbiased approach using the heterologous Escherichia
coli proteome now identifies the structural and sequence
determinants for caspase-3 substrates, revealing a kinetic threshold
that can distinguish relevant substrates.
Abstract: http://links.ealert.nature.com/ctt?kn=13&m=34130576&r=MTc2OTcxOTY5MQS2&b=2&j=NTkwMzM4NjAS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=12&m=34130576&r=MTc2OTcxOTY5MQS2&b=2&j=NTkwMzM4NjAS1&mt=1&rt=0
Tertiary structure checkpoint at anticodon loop modification in tRNA
functional maturation pp1109 - 1115
Sakurako Goto-Ito et al.
doi:10.1038/nsmb.1653
The maturation of tRNAs involves folding into their L shape and
nucleotide modifications at several positions. Some modifying
enzymes require an L-shaped substrate, and the crystal structure
of methylase Trm5 in complex with AdoMet and tRNA now reveals how
the substrate tertiary structure is sensed.
Abstract: http://links.ealert.nature.com/ctt?kn=16&m=34130576&r=MTc2OTcxOTY5MQS2&b=2&j=NTkwMzM4NjAS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=15&m=34130576&r=MTc2OTcxOTY5MQS2&b=2&j=NTkwMzM4NjAS1&mt=1&rt=0
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